How Can We Use Genomics to Improve Cereals with Rice as a Reference Genome?

Rice serves as a model crop for cereal genomics. The availability of complete genome sequences, together with various genomic resources available for both rice and Arabidopsis, have revolutionized our understanding of the genetic make-up of crop plants. Both macrocolinearity revealed by comparative mapping and microcolinearity revealed by sequence comparisons among the grasses indicate that sequencing and functional analysis of the rice genome will have a significant impact on other cereals in terms of both genomic studies and crop improvement. The availability of mutants, introgression libraries, and advanced transformation techniques make functional genomics in rice and other cereals more manageable than ever before. A wide array of genetic markers, including anchor markers for comparative mapping, SSRs and SNPs are widely used in genetic mapping, germplasm evaluation and marker assisted selection. An integrated database that combines genome information for rice and other cereals is key to the effective utilization of all genomics resources for cereal improvement. To maximize the potential of genomics for plant breeding, experiments must be further miniaturized and costs must be reduced. Many techniques, including targeted gene disruption or allele substitution, insertional mutagenesis, RNA interference and homologous recombination, need to be refined before they can be widely used in functional genomic analysis and plant breeding.     

Recombinase-directed plant transformation for the post-genomic era

Plant genomics promises to accelerate genetic discoveries for plant improvements. Machine-driven technologies are ushering in gene structural and expressional data at an unprecedented rate. Potential bottlenecks in this crop improvement process are steps involving plant transformation. With few exceptions, genetic transformation is an obligatory final step by which useful traits are engineered into plants. In addition, transgenesis is most often needed to confirm gene function, after deductions made through comparative genomics, expression profiles, and mutation analysis. This article reviews the use of recombinase systems to deliver DNA more efficiently into the plant genome.     

Bioinformatics: harvesting information for plant and crop science

Bioinformatics is an integral aspect of plant and crop science research. Developments in data management and analytical software are reviewed with an emphasis on applications in functional genomics. This includes information resources for Arabidopsis and crop species, and tools available for analysis and visualisation of comparative genomic data. Approaches used to explore relationships between plant genes and expressed sequences are compared, including use of ontologies. The impact of bioinformatics in forward and reverse genetics is described, together with the potential from data mining. The role of bioinformatics is explored in the wider context of plant and crop science.     

Need for multidisciplinary research towards a second green revolution

Despite recent achievements in conventional plant breeding and genomics, the rate of increase of crop yields is declining and thus there is a need for a second green revolution. Advances within single disciplines, alone, cannot solve the challenges of increasing yield. As scientific disciplines have become increasingly diversified, a more complete understanding of the mechanisms by which genetic and environmental variation modify grain yield and composition is needed, so that specific quantitative and quality targets can be identified. To achieve this aim, the expertise of plant genomics, physiology and agronomy, as well as recently developed plant modelling techniques, must be combined. There has been recent progress in these individual disciplines, but multidisciplinary approaches must be implemented to tackle drought stress and salinity as major constraints to achieving sufficient grain yield in the future.     

Applying modelling experiences from the past to shape crop systems biology: the need to converge crop physiology and functional genomics

Functional genomics has been driven greatly by emerging experimental technologies. Its development as a scientific discipline will be enhanced by systems biology, which generates novel, quantitative hypotheses via modelling. However, in order to better assist crop improvement, the impact of developing functional genomics needs to be assessed at the crop level, given a projected diminishing effect of genetic alteration on phenotypes from the molecule to crop levels. This review illustrates a recently proposed research field, crop systems biology, which is located at the crossroads of crop physiology and functional genomics, and intends to promote communications between the two. Past experiences with modelling whole-crop physiology indicate that the layered structure of biological systems should be taken into account. Moreover, modelling not only plays a role in data synthesis and quantitative prediction, but certainly also in heuristics and system design. These roles of modelling can be applied to crop systems biology to enhance its contribution to our understanding of complex crop phenotypes and subsequently to crop improvement. The success of crop systems biology needs commitments from scientists along the entire knowledge chain of plant biology, from molecule or gene to crop and agro-ecosystem.     

A special issue on ＂Plant Molecular Biology＂

The use of molecular biology and genomics tools in plant biology research has greatly expanded our understandingof the molecular mechanisms that underlie plant development and physiology.The successful establishment of researchresources such as mutant populations has led to progress in a variety of fields,including plant reproductive develop-ment,signal transduction,hormone functions,defense responses and epigenetic control.In the future these advanceswill potentially facilitate crop improvement through molecular breeding.     

TILLING by Sequencing (TbyS) for targeted genome mutagenesis in crops

TILLING (Targeting Induced Local Lesions in Genomes) by Sequencing (TbyS) refers to the application of high-throughput sequencing technologies to mutagenised TILLING populations as a tool for functional genomics. TbyS can be used to identify and characterise induced variation in genes (controlling traits of interest) within large mutant populations, and is a powerful approach for the study and harnessing of genetic variation in crop breeding programmes. The extension of existing TILLING platforms by TbyS will accelerate crop functional genomics studies, in concert with the rapid increase in genome editing capabilities and the number and quality of sequenced crop plant genomes. In this mini-review, we provide an overview of the growth of TbyS and its potential applications to crop molecular breeding.     

Integrating genomics and metabolomics for engineering plant metabolic pathways

Plant metabolites are characterized by an enormous chemical diversity, every plant having its own complex set of metabolites. This variety poses analytical challenges, both for profiling multiple metabolites in parallel and for the quantitative analysis of selected metabolites. We are only just starting to understand the roles of these metabolites, many of them being involved in adaptations to specific ecological niches and some finding beneficial use (e.g. as pharmaceuticals). Spectacular advances in plant metabolomics offer new possibilities, together with the aid of systems biology, to explore the extraordinary complexity of the plant biochemical capacity. State-of-the art genomics tools can be combined with metabolic profiling to identify key genes that could be engineered for the production of improved crop plants.     

Integrated physiological and agronomic modelling of N capture and use within the plant

Today farmers have several constraints to take into account in managing their crops: (i) competitiveness: productivity must be maintained or increased whereas inputs must be decreased, (ii) the environmental consequences of cultural practices: pesticide and fertilizer use must be decreased, and (iii) product quality must be improved and nitrogen nutrition is an important factor in harvest quality. These new constraints sometimes conflict: maximum yield is often obtained with large amounts of N, increasing the risks of N leaching. The determination of rates and dates for nitrogen application must become more precise in this context. Tools are required for the forecasting of crop requirements, the diagnosis of N deficiencies during the crop cycle and breeding of new adapted varieties. Models and diagnosis indicators have been developed to meet these needs, but those relating to nitrogen are often based on empirical relationships. Moreover, the available models and indicators often fail to account for cultivar-specific responses. The improvement of agronomic tools and the breeding of new varieties adapted to new cropping systems should be based on a thorough understanding of the key metabolic processes involved, and the relative contributions of these processes to yield determination in conditions of fluctuating N supply. For both purposes, more information is required about plant and crop N economy. In this paper, the way in which N absorption and use within the plant and crop, plant responses to deficiencies and excesses of nitrogen are taken into account in major agronomic models is described first. The level of sophistication of the modules comprising these models depends on operational objectives. Secondly, the ways in which the most recent molecular plant physiology findings can, and indeed should, be integrated into models at the crop and crop cycle levels are described. The potential value of this approach for improving current agronomic models and diagnostic tools, and for breeding more efficient varieties is also discussed.     

Quantitative proteomics to study the response of wheat to contrasting fertilisation regimes

Negative environmental impacts from mineral fertilisers and pesticides used in conventional cropping have raised concern over the sustainability of arable crop production. Organic cropping uses alternatives that avoid many of these negative environmental effects; however, crop yields can be significantly reduced, possibly due to a lower proportion of plant-available nutrients. To gain insights into the molecular effects of organic compared to conventional cropping systems on plant utilisation of nutrients, we used proteomics to analyse winter wheat (Triticum aestivum). Our aim was to investigate the effects of contrasting fertility management and crop protection regimes in organic and conventional cropping systems on the wheat flag leaf proteome and the association between the proteome and physiological traits. Wheat flag leaves were flash-frozen, lyophilised and milled prior to protein extraction (TCA/acetone) and analysed using 2D gel electrophoresis and MALDI-TOF MS. The abundance of 111 protein spots varied significantly between fertilisation regimes. Flag leaf N and P composition were significant drivers of differences in protein spot abundance, including major proteins involved in nitrogen remobilisation, photosynthesis, metabolism and stress response. These results indicate that molecular-based mechanisms are involved in the effect of contrasting cropping systems on nutrient utilisation and wheat grain yield. Using a functional genomics approach, we were able to identify proteins that are linked to causal genes, enabling the potential development of functional molecular markers for crop improvement in nutrient use efficiency.     

Genetic resources offer efficient tools for rice functional genomics research

Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in understanding the function of rice genes has lagged, hampering the utilization of rice genes for cereal crop improvement. The use of transfer DNA (T‐DNA) insertional mutagenesis offers the advantage of uniform distribution throughout the rice genome, but preferentially in gene‐rich regions, resulting in direct gene knockout or activation of genes within 20–30 kb up‐ and downstream of the T‐DNA insertion site and high gene tagging efficiency. Here, we summarize the recent progress in functional genomics using the T‐DNA‐tagged rice mutant population. We also discuss important features of T‐DNA activation‐ and knockout‐tagging and promoter‐trapping of the rice genome in relation to mutant and candidate gene characterizations and how to more efficiently utilize rice mutant populations and datasets for high‐throughput functional genomics and phenomics studies by forward and reverse genetics approaches. These studies may facilitate the translation of rice functional genomics research to improvements of rice and other cereal crops.     

Plant–microbes interactions in enhanced fertilizer-use efficiency

The continued use of chemical fertilizers and manures for enhanced soil fertility and crop productivity often results in unexpected harmful environmental effects, including leaching of nitrate into ground water, surface run-off of phosphorus and nitrogen run-off, and eutrophication of aquatic ecosystems. Integrated nutrient management systems are needed to maintain agricultural productivity and protect the environment. Microbial inoculants are promising components of such management systems. This review is a critical summary of the efforts in using microbial inoculants, including plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi for increasing the use efficiency of fertilizers. Studies with microbial inoculants and nutrients have demonstrated that some inoculants can improve plant uptake of nutrients and thereby increase the use efficiency of applied chemical fertilizers and manures. These proofs of concept studies will serve as the basis for vigorous future research into integrated nutrient management in agriculture.     

European plant science: a field of opportunities

Plants have a pivotal role in eco- and agricultural systems.Genomics is driving a rapid expansion of our understanding ofhow genes, individually and in networks, determine plant function.Technological developments in breeding and genomics are providingstrategies to translate this knowledge into crop improvement.The possibilities range from improvement of existing crops andthe systematic use of natural diversity through to the domesticationof completely new species. As examples of possible goals, itis discussed how profiling of composition will integrate plantbreeding and agronomic practice with emerging knowledge aboutnutrition and health, how improved and novel crops will contributeto the creation of new bio-based economies revolving aroundplant products, and how advances in our knowledge about plant–environmentand plant–pathogen interactions will provide novel strategiesto stabilize agricultural yield in a fluctuating environmentand contribute to integrated approaches in which modern agricultureis carried out in concert with the environment. In addition,knowledge generated by plant science will be needed to monitor,understand, and cope with climate change and its impact on agricultureand ecosystems. Realization of these goals will require closeinteractions with related disciplines including agronomy andecology. Further, it will be important to continue and deepenopen support for research in the developing world. Key words: Agronomic practice, biodiversity, domestication, ecosystems, environment, genomics, novel crops, plant breeding, plant products, yield     

Lotus japonicus as a platform for legume research

The major role of 'model plants' is to provide knowledge and technologies obtained in related systems to researchers studying crop plants. Lotus japonicus was chosen as a model system first for legume genetics and then for legume genomics. A large number of L. japonicus mutants that have alterations in legume-specific phenomena have been generated and phenotypically characterized, and genomics has drastically accelerated the molecular characterization of these mutants. Substantial resources of information and experimental materials, including genomic and cDNA sequences, corresponding DNA libraries and high-density linkage maps demonstrate that L. japonicus is an excellent model system. Transfer of knowledge from L. japonicus to other legumes, especially crop legumes, is a matter for urgent consideration.     

Utilisation of plant functional diversity in wildflower strips for the delivery of multiple agroecosystem services

Increased plant diversity in cropping systems can play an important role in agriculture by enhancing arthropod‐mediated ecosystem services, including biological control and pollination. However, there is limited research investigating the concurrent influence of plant functional diversity within cultivated systems on different arthropod functional groups, the provision of multiple ecosystem services, and crop yield. During a field experiment, repeated over 2 years, we measured the effect of increasing plant functional diversity on community structure of arthropod visitors, the abundance of multiple pests and induced crop damage, and fruit production in two varieties of tomato. Plant resources (floral and extra‐floral nectar and pollen) were included within experimental plots in four levels, with each level increasing the plant functional group richness, based on floral morphology and availability of resources, in a replacement series. The presence of sown flower mixtures in experimental plots was associated with increased abundance and diversity of natural enemy functional groups and an enhanced abundance of bees (Hymenoptera: Apiformes). However, we only detected relatively small variability in arthropod visitors among types of mixtures, and increased abundance of natural enemies did not translate into stronger pest suppression or reduced crop damage. Lepidoptera pest damage was significantly higher in plots adjacent to wildflower strips, an ecosystem disservice, but a significantly higher crop productivity was recorded from these plots. Our results provide evidence that inclusion of non‐crop plant resources in agroecosystems can improve the conservation of beneficial arthropods and may lead to increased crop productivity.     

Invited review: Transformation of strawberry: The basis for translational genomics in Rosaceae

Summary Translational genomics is defined as the application of molecular-genetic principles derived from model systems to species of experimental or economic interest. The past 20 years of research in plant model systems such as Arabidopsis thaliana have relinquished vast amounts of information regarding gene function, the integration of genetic components into pathways, and the interrelationships between pathways to control form and function in plants and plant-products alike. At present, the challenge is to relate these paradigms to other species of economic or scientific interest. Apart from being an important and valuable crop, strawberry (Fragaria spp.) is a member of the Rosaceae, a plant family containing fruit, nut, ornamental and wood-bearing species. Strawberry is unique within the Rosaceae in that it is a rapidly growing herbaceous perennial with a small genome and the ability to thrive in a laboratory setting. Strawberry species may also be transformed and regenerated in a time scale of weeks or months instead of years. For these reasons, strawberry has been recognized as the translational genomics model for the Rosaceae family. This review summarizes and synthesizes the technical reports of strawberry regeneration and transformation, consolidating the large body of information regarding genetic modification of this important genus.     

Crop genomics: advances and applications

The completion of reference genome sequences for many important crops and the ability to perform high-throughput resequencing are providing opportunities for improving our understanding of the history of plant domestication and to accelerate crop improvement. Crop plant comparative genomics is being transformed by these data and a new generation of experimental and computational approaches. The future of crop improvement will be centred on comparisons of individual plant genomes, and some of the best opportunities may lie in using combinations of new genetic mapping strategies and evolutionary analyses to direct and optimize the discovery and use of genetic variation. Here we review such strategies and insights that are emerging.